replace_to_na() was made defunct, please use replace_with_na() instead. (see 242)

Minor changes

miss_var_cumsum and miss_case_cumsum are now exported

use map_dfc instead of map_df

Fix various extra warnings and improve test coverage

Bug Fixes

Address bug where the number of missings in a row is not calculated properly - see 238 and 232. The solution involved using rowSums(is.na(x)), which was 3 times faster.

Resolve bug in gg_miss_fct() where warning is given for non explicit NA values - see 241.

skip vdiffr tests on github actions

use tibble() not data_frame()

naniar 0.4.2 (2019/02/15) “The Planting of The Tree”

Improvements

The geom_miss_point()ggplot2 layer can now be converted into an interactive web-based version by the ggplotly() function in the plotly package. In order for this to work, naniar now exports the geom2trace.GeomMissPoint() function (users should never need to call geom2trace.GeomMissPoint() directly – ggplotly() calls it for you).

Dependency fixes

This fixes two problems that were identified as part of reverse dependency checks of dplyr 0.8.0 release candidate. https://github.com/tidyverse/dplyr/blob/revdep_dplyr_0_8_0_RC/revdep/problems.md#naniar

n() must be imported or prefixed like any other function. In the PR, I’ve changed 1:n() to dplyr::row_number() as naniar seems to prefix all dplyr functions.

update_shadow was only restoring the class attributes, changed so that it restores all attributes, this was causing problems when data was a grouped_df. This likely was a problem before too, but dplyr 0.8.0 is stricter about what is a grouped data frame.

naniar 0.4.1 (2018/12/14)

Minor Changes

pkgdown updates: update favicon and logo, set up for gh-pages deployment

use a scalar integer in new_tibble

naniar 0.4.1 (2018/11/20) “Aslan’s Song”

Minor Change

naniar 0.4.0 (2018/09/10) “An Unexpected Meeting”

New Feature

Add custom label support for missings and not missings with functions add_label_missings and add_label_shadow() and add_any_miss(). So you can now do `add_label_missings(data, missing = “custom_missing_label”, complete = “custom_complete_label”)

impute_median() and scoped variants

any_shade() returns a logical TRUE or FALSE depending on if there are any shade values

nabular() an alias for bind_shadow() to tie the nabular term into the work.

is_nabular() checks if input is nabular.

geom_miss_point() now gains the arguments from shadow_shift()/impute_below() for altering the amount of jitter and proportion below (prop_below).

miss_var_summary and miss_case_summary now no longer provide the cumulative sum of missingness in the summaries - this summary can be added back to the data with the option add_cumsum = TRUE. #186

Added gg_miss_upset to replace workflow of:

data %>%
as_shadow_upset() %>%
UpSetR::upset()

Major Change

recode_shadow now works! This function allows you to recode your missing values into special missing values. These special missing values are stored in the shadow part of the dataframe, which ends in _NA.

implemented shade where appropriate throughout naniar, and also added verifiers, is_shade, are_shade, which_are_shade, and removed which_are_shadow.

as_shadow and bind_shadow now return data of class shadow. This will feed into recode_shadow methods for flexibly adding new types of missing data.

Note that in the future shadow might be changed to nabble or something similar.

Minor feature

Functions add_label_shadow() and add_label_missings() gain arguments so you can only label according to the missingness / shadowy-ness of given variables.

new function which_are_shadow(), to tell you which values are shadows.

new function long_shadow(), which converts data in shadow/nabular form into a long format suitable for plotting. Related to #165

Added tests for miss_scan_count

Minor Changes

gg_miss_upset gets a better default presentation by ordering by the largest intersections, and also an improved error message when data with only 1 or no variables have missing values.

shadow_shift gains a more informative error message when it doesn’t know the class.

Changed common_na_string to include escape characters for “?”, “", "." so that if they are used in replacement or searching functions they don’t return the wildcard results from the characters "?", "”, and “.”.

miss_case_table and miss_var_table now has final column names pct_vars, and pct_cases instead of pct_miss - fixes #178.

Breaking Changes

Deprecated old names of the scalar missingness summaries, in favour of a more consistent syntax #171. The old the and new are:

old_names

new_names

miss_case_pct

pct_miss_case

miss_case_prop

prop_miss_case

miss_var_pct

pct_miss_var

miss_var_prop

prop_miss_var

complete_case_pct

pct_complete_case

complete_case_prop

prop_complete_case

complete_var_pct

pct_complete_var

complete_var_prop

prop_complete_var

These old names will be made defunct in 0.5.0, and removed completely in 0.6.0.

impute_below has changed to be an alias of shadow_shift - that is it operates on a single vector. impute_below_all operates on all columns in a dataframe (as specified in #159)

Bug fix

Ensured that miss_scan_count actually return’d something.

gg_miss_var(airquality) now prints the ggplot - a typo meant that this did not print the plot

naniar 0.3.1 (2018/06/10) “Strawberry’s Adventure”

Minor Change

This is a patch release that removes tidyselect from the package Imports, as it is unnecessary. Fixes #174

# naniar 0.3.0 (2018/06/06) “Digory and his Uncle Are Both in Trouble”

New Features

Added all_miss() / all_na() equivalent to all(is.na(x))

Added any_complete() equivalent to all(complete.cases(x))

Added any_miss() equivalent to anyNA(x)

Added common_na_numbers and finalised common_na_strings - to provide a list of commonly used NA values #168

Added miss_var_which, to lists the variable names with missings

Added as_shadow_upset which gets the data into a format suitable for plotting as an UpSetR plot:

airquality %>%as_shadow_upset() %>%UpSetR::upset()

Added some imputation functions to assist with exploring missingness structure and visualisation:

impute_below Perfoms as for shadow_shift, but performs on all columns. This means that it imputes missing values 10% below the range of the data (powered by shadow_shift), to facilitate graphical exloration of the data. Closes #145 There are also scoped variants that work for specific named columns: impute_below_at, and for columns that satisfy some predicate function: impute_below_if.

Added unbind_shadow and unbind_data as helpers to remove shadow columns from data, and data from shadows, respectively.

Added is_shadow and are_shadow to determine if something contains a shadow column. simimlar to rlang::is_na and rland::are_na, is_shadow this returns a logical vector of length 1, and are_shadow returns a logical vector of length of the number of names of a data.frame. This might be revisited at a later point (see any_shade in add_label_shadow).

Aesthetics now map as expected in geom_miss_point(). This means you can write things like geom_miss_point(aes(colour = Month)) and it works appropriately. Fixed by Luke Smith in Pull request #144, fixing #137.

Minor Changes

miss_var_summary and miss_case_summary now return use order = TRUE by default, so cases and variables with the most missings are presented in descending order. Fixes #163

Changes for Visualisation:

Changed the default colours used in gg_miss_case and gg_miss_var to lorikeet purple (from ochRe package: https://github.com/ropenscilabs/ochRe)

Added some detail on alternative methods for replacing with NA in the vignette “replacing values with NA”.

# naniar 0.2.0 (2018/02/08) (“The First Joke and Other Matters”)

New Features

Speed improvements. Thanks to the help, contributions, and discussion with Romain François and Jim Hester, naniar now has greatly improved speed for calculating the missingness in each row. These speedups should continue to improve in future releases.

New “scoped variants” of replace_with_na, thankyou to Colin Fay for his work on this:

replace_with_na_all replaces all NAs across the dataframe that meet a specified condition (using the syntax ~.x == -99)

replace_with_na_at replaces all NAs across for specified variables

replace_with_na_if replaces all NAs for those variables that satisfy some predicate function (e.g., is.character)

added which_na - replacement for which(is.na(x))

miss_scan_count. This makes it easier for users to search for particular occurrences of these values across their variables. #119

n_miss_row calculates the number of missing values in each row, returning a vector. There are also 3 other functions which are similar in spirit: n_complete_row, prop_miss_row, and prop_complete_row, which return a vector of the number of complete obserations, the proportion of missings in a row, and the proportion of complete obserations in a row

add_miss_cluster is a new function that calculates a cluster of missingness for each row, using hclust. This can be useful in exploratory modelling of missingness, similar to Tierney et al 2015: “doi: 10.1136/bmjopen-2014-007450” and Barnett et al. 2017: “doi: 10.1136/bmjopen-2017-017284”

Now exported where_na - a function that returns the positions of NA values. For a dataframe it returns a matrix of row and col positions of NAs, and for a vector it returns a vector of positions of NAs. (#105)

Minor changes

Updated the vignette “Gallery of Missing Data Visualisations” to include the facet features and order_cases.

bind_shadow gains a only_miss argument. When set to FALSE (the default) it will bind a dataframe with all of the variables duplicated with their shadow. Setting this to TRUE will bind variables only those variables that contain missing values.

Cleaned up the visualisation of gg_miss_case to be clearer and less cluttered ( #117), also added n order_cases option to order by cases.

Added a facet argument to gg_miss_var, gg_miss_case, and gg_miss_span. This makes it easier for users to visualise these plots across the values of another variable. In the future I will consider adding facet to the other shorthand plotting function, but at the moment these seemed to be the ones that would benefit the most from this feature.

Bug fix

oceanbuoys now is numeric type for year, latitude, and longitude, previously it was factor. See related issue

Improved handling of shadow_shift when there are Inf or -Inf values (see #117)

Breaking change

Deprecated replace_to_na, with replace_with_na, as it is a more natural phrase (“replace coffee to tea” vs “replace coffee with tea”). This will be made defunct in the next version.

cast_shadow no longer works when called as cast_shadow(data). This action used to return all variables, and then shadow variables for the variables that only contained missing values. This was inconsistent with the use of cast_shadow(data, var1, var2). A new option has been added to bind_shadow that controls this - discussed below. See more details at issue 65.

Change behaviour of cast_shadow so that the default option is to return only the variables that contain missings. This is different to bind_shadow, which binds a complete shadow matrix to the dataframe. A way to think about this is that the shadow is only cast on variables that contain missing values, whereas a bind is binding a complete shadow to the data. This may change in the future to be the default option for bind_shadow.

Minor Changes

Update vignettes to have floating menu and better figure size.

minor changes to graphics in gg_miss_fct - change legend title from “Percent Missing” to “% Miss”.

# naniar 0.1.0 (2017/08/09) “The Founding of naniar”

This is the first release of naniar onto CRAN, updates to naniar will happen reasonably regularly after this approximately every 1-2 months

# narnia 0.0.9.9400 (2017/07/24)

new features

replace_to_na is a complement to tidyr::replace_na and replaces a specified value from a variable to NA.

gg_miss_fct returns a heatmap of the number of missings per variable for each level of a factor. This feature was very kindly contributed by Colin Fay.

gg_miss_ functions now return a ggplot object, which behave as such. gg_miss_ basic themes can be overriden with ggplot functions. This fix was very kindly contributed by Colin Fay.

removed defunct functions as per #63

made add_* functions handle bare unqouted names where appropriate as per #61

added tests for the add_* family

got the svgs generated from vdiffr, thanks @karawoo!

breaking changes

changed geom_missing_point() to geom_miss_point(), to keep consistent with the rest of the functions in naniar.

# narnia 0.0.8.9100 (2017/06/23)

new features

updated datasets brfss and tao as per #59

# narnia 0.0.7.9992 (2017/06/22)

new features

add_label_missings()

add_label_shadow()

cast_shadow()

cast_shadow_shift()

cast_shadow_shift_label()

added github issue / contribution / pull request guides

ts generic functions are now miss_var_span and miss_var_run, and gg_miss_span and work on data.frame’s, as opposed to just ts objects.

add_shadow_shift() adds a column of shadow_shifted values to the current dataframe, adding "_shift" as a suffix

cast_shadow() - acts like bind_shadow() but allows for specifying which columns to add

shadow_shift now has a method for factors - powered by forcats::fct_explicit_na() #3

bug fixes

shadow_shift.numeric works when there is no variance (#37)

name changes

changed is_na function to label_na

renamed most files to have tidy-miss-[topic]

gg_missing_* is changed to gg_miss_* to fit with other syntax

Removed functions

Removed old functions miss_cat, shadow_df and shadow_cat, as they are no longer needed, and have been superceded by label_missing_2d, as_shadow, and is_na.

minor changes

drastically reduced the size of the pedestrian dataset, consider 4 sensor locations, just for 2016.

New features

New dataset, pedestrian - contains hourly counts of pedestrians

First pass at time series missing data summaries and plots:

miss_ts_run(): return the number of missings / complete in a single run

miss_ts_summary(): return the number of missings in a given time period

gg_miss_ts(): plot the number of missings in a given time period

Name changes

renamed package from naniar to narnia - I had to explain the spelling a few times when I was introducing the package and I realised that I should change the name. Fortunately it isn’t on CRAN yet.

# naniar 0.0.6.9100 (2017/03/21)

Added prop_miss and the complement prop_complete. Where n_miss returns the number of missing values, prop_miss returns the proportion of missing values. Likewise, prop_complete returns the proportion of complete values.

Defunct functions

As stated in 0.0.5.9000, to address Issue #38, I am moving towards the format miss_type_value/fun, because it makes more sense to me when tabbing through functions.

These will be made defunct in the next release, 0.0.6.9000 (“The Wood Between Worlds”).

# naniar 0.0.4.9000 (2016/12/31)

New features

n_complete is a complement to n_miss, and counts the number of complete values in a vector, matrix, or dataframe.

Bug fixes

shadow_shift now handles cases where there is only 1 complete value in a vector.

Other changes

added much more comprehensive testing with testthat.

# naniar 0.0.3.9901 (2016/12/18)

After a burst of effort on this package I have done some refactoring and thought hard about where this package is going to go. This meant that I had to make the decision to rename the package from ggmissing to naniar. The name may strike you as strange but it reflects the fact that there are many changes happening, and that we will be working on creating a nice utopia (like Narnia by CS Lewis) that helps us make it easier to work with missing data

New Features (under development)

add_n_miss and add_prop_miss are helpers that add columns to a dataframe containing the number and proportion of missing values. An example has been provided to use decision trees to explore missing data structure as in “doi: 10.1136/bmjopen-2014-007450”

more shadows. These are mainly around bind_shadow and gather_shadow, which are helper functions to assist with creating

Bug fixes

geom_missing_point() broke after the new release of ggplot2 2.2.0, but this is now fixed by ensuring that it inherits from GeomPoint, rather than just a new Geom. Thanks to Mitchell O’hara-Wild for his help with this.

missing data summaries table_missing_var and table_missing_case also now return more sensible numbers and variable names. It is possible these function names will change in the future, as these are kind of verbose.

semantic versioning was incorrectly entered in the DESCRIPTION file as 0.2.9000, so I changed it to 0.0.2.9000, and then to 0.0.3.9000 now to indicate the new changes, hopefully this won’t come back to bite me later. I think I accidentally did this with visdat at some point as well. Live and learn.

Other changes

gathered related functions into single R files rather than leaving them in their own.

correctly imported the %>% operator from magrittr, and removed a lot of chaff around @importFrom - really don’t need to use @importFrom that often.

# ggmissing 0.0.2.9000 (2016/07/29)

New Feature (under development)

geom_missing_point() now works in a way that we expect! Thanks to Miles McBain for working out how to get this to work.

# ggmissing 0.0.1.9000 (2016/07/29)

New Feature (under development)

tidy summaries for missing data:

percent_missing_df returns the percentage of missing data for a data.frame

percent_missing_var the percentage of variables that contain missing values

percent_missing_case the percentage of cases that contain missing values.